In terms of organisation RAF Wyton was part of the combined station RAF Brampton Wyton Henlow, a merger of Wyton with two previously separate bases, RAF Brampton and RAF Henlow. Wyton is the largest of the three. It is home to Equipment Support (Air) and Corporate Technical Services. The airfield is now decommissioned but was used for flight training by 57(R) Squadron EFT, the University Air Squadrons of London and Cambridge and No. 5 Air Experience Flight.

The Victor belonged to a separate Radar Reconnaissance Flight (initially of one aircraft - rising to three by the time RRF was disbanded in 1962) to supplement the work of the Valiants of 543 Sqn. The Canberras of 58 Sqn were a mix of PR7 and PR 9s.

Also based at RAF Wyton were the T17 and T17A Canberras of 360 Sqn, the only joint RAF and RN Squadron specialising in ECM training. In the early 90's one of its pilots was Ft Lt Rory Underwood. Other residents at RAF Wyton were 100 Sqn with a mixture of Canberra types in the Targeting Role. Also resident but "never officially present" were the three Nimrod R1s belonging to 51 Sqn used in the Elint and Sigint role.

During the middle 1990s, RAF Wyton hosted an RAF-sponsored microlight club. Consisting of a small group of flex-wing microlight and 3-axis aircraft, there was a thriving flight school with two instructors, the former Chief Inspector of the BMAA David Marshall and the training instructor pilot Paul Foggoa. The school was based in the old crash building - the original purpose of which was to house the crash-rescue fire engines. The success of the club, and the inclusion of non-RAF members, led to the club expanding to the corner of one of the large hangars.

In the mid-1990s the two stations of RAF Wyton and RAF Brampton amalgamated to become RAF Brampton/Wyton. In 2001 RAF Henlow joined RAF Brampton Wyton making the tri site of RAF Brampton Wyton Henlow. At the time it was the largest Station in terms of both geography and number of personnel in the RAF.

The 2010 Strategic Defence and Security Review announced the formation of Joint Forces Command (JFC), and on 2 April 2012, the RAF Brampton Wyton Henlow tri site was disbanded. JFC assumed responsibility for RAF Brampton/ Wyton, with RAF Henlow remaining under the control of Headquarters Air Command. The decision to close RAF Brampton by December 2013 led to the command and control of the Station transferring to RAF Wyton. RAF Brampton was renamed Brampton Camp and became a satellite unit of RAF Wyton.

Joining HQ JFIG and DGIFC at RAF Wyton from 2013 will be 42 Engineer Regiment. They will be accompanied by elements of Defence Human Intelligence and specialist staff from Defence Intelligence. These elements will come together to support worldwide operations from purpose-built facilities within the Pathfinder Building. In future years, other elements of JFIG and the wider Defence Intelligence community are expected to work together at Wyton.

No. 1 Intelligence Surveillance Reconnaissance Squadron of the RAF moved to Wyton from RAF Marham in April 2017.[28]

By 2014, RAF Wyton's population grew 5-fold to approximately 1,800 personnel, with every likelihood of a further 1,500-2,000 personnel joining before the end of the decade. Alongside the build-up of the Defence Intelligence footprint at RAF Wyton, the Station also plays host to several Lodger Units. The active airfield hosts the 57 (Reserve) Sqn Elementary Flying Training School, No. 5 Air Experience Flt, 2 University Air Squadrons (UAS) as well as the Pathfinder Flying Club. 57(R) Squadron is responsible for conducting Elementary Flying Training (EFT) for around 50 percent of the RAF's entry of new student pilots. Students arrive following completion of Initial Officer Training (IOT) at RAF Cranwell and remain for around 6 months of flying training on the Grob Tutor 115E. The course is broadly split into 2 phases. During the 1st phase, students are taught the basics of flying an aircraft, fly solo and learn general handling, including aerobatics. The 2nd phase of the course sees the students progress onto more advanced flying, including instrument flying, low level navigation and formation flying. The course culminates in a demanding final test, where all elements taught on the course can be assessed. Following the successful completion of this test, students are moved to either fast jet, rotary or multi engine to continue their flying training.

The 2 UAS's teach undergraduate students to fly to the standard of a Private pilot licence (PPL), with additional opportunities to fly Aerobatics, Formation Flying and Low Level Navigation.

The Defence Infrastructure Organisation (DIO) also has a large presence at Wyton with both its Operations Accommodation and International elements. DIO Ops Accommodation is responsible for the management of 49,000 Service Family Accommodation in the UK and infrastructure support for the United States Visiting Forces. DIO International looks after the International Estate used by Defence, including the maintenance and provision of facilities on the Permanent Joint Operating Bases.

DCMA International maintains a significant presence at Wyton. DCMA International established the headquarters for DCMA Northern Europe at Wyton in 2013. Shortly thereafter, in 2014, DCMA disestablished DCMA Northern Europe and established DCMA United Kingdom (UK). Since 2014, from its headquarters at Wyton, DCMA UK has been providing itinerant contract administration services throughout the UK, Northern Europe, and Scandinavia. In addition, DCMA UK manages its footprints in contractor plants from its headquarters at Wyton.